Additional data file 6.

THP-1 cells (1 × 106 cells) were transfected with an individual siRNA species against each of the TF genes. The total RNA was extracted 48 h after the transfection and used for qRT-PCR. The changes in expression levels (perturbations) were evaluated by CT calculated according to the method described by Livak et al. [37]. Quadruplicated experiments were carried out to obtain the average CT, SD and P-value. Only the edges that gave a low SD (mean of ΔΔCT > 2 SD) and P-value (< 0.05) were selected as significant regulatory TF-TF gene edges for preparing this table. 'Input gene' and 'target gene' indicates genes knocked down by a specific siRNA and genes perturbed significantly after siRNA transfection, respectively. 'Activate' and 'suppress' indicate that knockdown of one TF led to a significant decrease in the expression of another and to a significant increase in the expression of another, respectively. The actual data for RNAi perturbation are in Additional data file 4 (for all of the edges tested) and Additional data file 5 (for only significant edges).

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Tomaru et al. Genome Biology 2009 10:R121   doi:10.1186/gb-2009-10-11-r121